Magnesium in PDB 3oxd: Crystal Structure of Glycine Riboswitch with Two Mutations

The structure of Crystal Structure of Glycine Riboswitch with Two Mutations, PDB code: 3oxd was solved by L.Huang, A.Serganov, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.969, 83.969, 199.998, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 21.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 34;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Glycine Riboswitch with Two Mutations (pdb code 3oxd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 34 binding sites of Magnesium where determined in the Crystal Structure of Glycine Riboswitch with Two Mutations, PDB code: 3oxd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 34 in the Crystal Structure of Glycine Riboswitch with Two Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Glycine Riboswitch with Two Mutations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:0.2 occ:1.00 O A:HOH143 2.2 90.1 1.0 O A:HOH141 2.2 89.7 1.0 O A:HOH139 2.2 90.0 1.0 O A:HOH140 2.2 90.0 1.0 O A:HOH138 2.2 89.7 1.0 O A:HOH142 2.2 89.8 1.0 OP1 A:A34 3.7 74.9 1.0 OP2 A:C35 3.8 79.7 1.0 N7 A:G36 4.3 77.3 1.0 O6 A:G36 4.5 75.9 1.0 N6 A:A37 4.7 71.7 1.0

Magnesium binding site 2 out of 34 in the Crystal Structure of Glycine Riboswitch with Two Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Glycine Riboswitch with Two Mutations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:0.5 occ:1.00 OP2 A:A75 2.8 76.2 1.0 OP1 A:A22 3.2 67.2 1.0 P A:A75 3.7 75.3 1.0 OP1 A:A75 3.7 75.6 1.0 O3' A:A21 4.1 65.6 1.0 P A:A22 4.3 67.4 1.0 N7 A:A75 4.5 76.7 1.0 OP2 A:C74 4.6 75.2 1.0 OP1 A:C74 4.6 73.8 1.0 O3' A:C74 4.6 74.7 1.0 C8 A:A75 4.6 76.4 1.0 C3' A:C74 4.7 74.0 1.0 P A:C74 4.8 74.4 1.0 O5' A:C74 4.8 74.4 1.0

Magnesium binding site 3 out of 34 in the Crystal Structure of Glycine Riboswitch with Two Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Glycine Riboswitch with Two Mutations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:92.3 occ:1.00 OP2 A:A76 2.1 76.6 1.0 OP1 A:A75 2.7 75.6 1.0 O5' A:A75 3.4 74.7 1.0 P A:A76 3.5 76.5 1.0 P A:A75 3.7 75.3 1.0 OP1 A:C74 3.7 73.8 1.0 N6 A:A78 3.9 75.2 1.0 C5' A:C74 4.2 73.4 1.0 O5' A:A76 4.2 77.2 1.0 N7 A:A77 4.3 78.2 1.0 N6 A:A77 4.4 78.8 1.0 N7 A:A76 4.4 78.7 1.0 OP1 A:A76 4.4 76.0 1.0 O3' A:A75 4.5 76.0 1.0 C3' A:A75 4.5 75.5 1.0 O3' A:C74 4.5 74.7 1.0 C5' A:A75 4.6 75.2 1.0 C8 A:A76 4.7 78.2 1.0 C6 A:A78 4.7 75.7 1.0 OP2 A:A75 4.9 76.2 1.0 P A:C74 4.9 74.4 1.0 O5' A:C74 4.9 74.4 1.0 C4' A:C74 4.9 73.5 1.0

Magnesium binding site 4 out of 34 in the Crystal Structure of Glycine Riboswitch with Two Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Glycine Riboswitch with Two Mutations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:0.3 occ:1.00 N7 A:G72 3.9 78.0 1.0 OP2 A:A71 3.9 87.1 1.0 O6 A:G72 4.3 76.6 1.0 OP2 A:G72 4.5 83.2 1.0 O6 A:G73 4.5 75.5 1.0 C5 A:G72 4.7 76.5 1.0 P A:A71 4.7 88.2 1.0 C8 A:G72 4.8 78.0 1.0 N7 A:G73 4.8 73.8 1.0 O5' A:A71 4.8 86.3 1.0 C6 A:G72 4.8 75.8 1.0 OP1 A:A71 5.0 90.0 1.0

Magnesium binding site 5 out of 34 in the Crystal Structure of Glycine Riboswitch with Two Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Glycine Riboswitch with Two Mutations within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg106 b:90.8 occ:1.00 O A:HOH145 2.2 67.3 1.0 O B:HOH137 2.2 67.7 1.0 O B:HOH139 2.2 67.1 1.0 O A:HOH144 2.2 67.0 1.0 O B:HOH140 2.2 67.2 1.0 O B:HOH138 2.2 67.2 1.0 OP1 B:A33 4.2 59.9 1.0 O B:HOH156 4.3 58.4 1.0 OP1 A:C66 4.3 59.1 1.0 O4' B:A65 4.4 60.0 1.0 N7 B:A33 4.5 55.4 1.0 C4' B:A65 4.5 60.0 1.0 N3 A:A65 4.6 58.6 1.0 C1' A:A65 4.7 58.7 1.0 C8 B:A33 4.7 55.9 1.0 C2 B:A81 4.8 58.0 1.0 C1' B:A65 4.9 60.0 1.0 O3' B:A65 4.9 60.1 1.0 O B:HOH159 4.9 58.8 1.0 O2' A:A65 4.9 60.1 1.0

Magnesium binding site 6 out of 34 in the Crystal Structure of Glycine Riboswitch with Two Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Glycine Riboswitch with Two Mutations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:73.9 occ:1.00 O A:HOH148 2.2 31.3 1.0 O A:HOH149 2.2 30.6 1.0 O A:HOH151 2.2 31.5 1.0 O A:HOH146 2.2 31.3 1.0 O A:HOH147 2.2 31.1 1.0 O A:HOH150 2.2 31.1 1.0 O6 A:G47 3.9 79.9 1.0 O4 A:U46 3.9 77.6 1.0 N4 A:C48 4.2 79.9 1.0 O6 A:G55 4.3 76.1 1.0 N4 A:C54 4.6 73.4 1.0 C4 A:U46 4.7 79.7 1.0 C5 A:U46 4.9 81.5 1.0 C6 A:G47 5.0 82.0 1.0

Magnesium binding site 7 out of 34 in the Crystal Structure of Glycine Riboswitch with Two Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Glycine Riboswitch with Two Mutations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg110 b:65.9 occ:1.00 OP2 A:A21 2.0 66.9 1.0 O A:HOH155 2.2 31.6 1.0 O A:HOH156 2.2 31.9 1.0 O A:HOH153 2.2 32.1 1.0 O A:HOH152 2.2 31.8 1.0 O A:HOH154 2.2 32.3 1.0 P A:A21 3.5 65.6 1.0 O5' A:A21 4.0 64.1 1.0 O A:HOH167 4.1 47.7 1.0 N7 A:A22 4.2 68.2 1.0 O4 A:U23 4.3 71.9 1.0 OP1 A:A21 4.4 66.1 1.0 C5' A:U20 4.4 70.5 1.0 O3' A:U20 4.4 65.9 1.0 C3' A:U20 4.4 66.3 1.0 N7 A:A21 4.4 62.6 1.0 N6 A:A22 4.5 70.6 1.0 C8 A:A21 4.7 62.3 1.0 O2 A:U19 4.8 86.2 1.0 O5' A:U20 4.9 73.5 1.0

Magnesium binding site 8 out of 34 in the Crystal Structure of Glycine Riboswitch with Two Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Glycine Riboswitch with Two Mutations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg111 b:79.2 occ:1.00 O A:HOH160 2.2 39.4 1.0 O A:HOH161 2.2 39.3 1.0 O A:HOH159 2.2 39.4 1.0 O A:HOH158 2.2 39.6 1.0 O A:HOH162 2.2 39.4 1.0 O A:HOH157 2.2 39.4 1.0 N7 A:G25 4.1 91.5 1.0 N7 A:G26 4.2 0.5 1.0 O6 A:G26 4.4 96.8 1.0 C5 A:C24 4.7 78.7 1.0 N4 A:C24 4.7 78.0 1.0 O6 A:G25 4.7 89.2 1.0 C4 A:C24 4.8 79.1 1.0 C8 A:G25 4.9 93.1 1.0 C5 A:G25 4.9 92.3 1.0

Magnesium binding site 9 out of 34 in the Crystal Structure of Glycine Riboswitch with Two Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Glycine Riboswitch with Two Mutations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg112 b:81.7 occ:1.00 O A:HOH163 2.2 48.0 1.0 O A:HOH167 2.2 47.7 1.0 O A:HOH165 2.2 47.6 1.0 O A:HOH166 2.2 47.5 1.0 O A:HOH164 2.2 47.9 1.0 OP2 A:U20 2.5 77.0 1.0 O5' A:U20 3.0 73.5 1.0 P A:U20 3.2 76.4 1.0 O3' A:U19 3.5 79.1 1.0 OP1 A:A21 3.8 66.1 1.0 O2' A:U19 4.3 82.4 1.0 C5' A:U20 4.4 70.5 1.0 O3' A:U20 4.4 65.9 1.0 C3' A:U19 4.5 82.4 1.0 P A:A21 4.5 65.6 1.0 OP1 A:U20 4.6 76.2 1.0 OP2 A:C15 4.6 82.0 1.0 OP2 A:A21 4.7 66.9 1.0 C4' A:U20 4.9 67.5 1.0

Magnesium binding site 10 out of 34 in the Crystal Structure of Glycine Riboswitch with Two Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Glycine Riboswitch with Two Mutations within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg113 b:84.1 occ:1.00 O B:HOH145 2.2 53.0 1.0 O B:HOH142 2.2 52.2 1.0 O B:HOH141 2.2 53.0 1.0 O B:HOH144 2.2 52.8 1.0 O B:HOH143 2.2 52.9 1.0 N7 B:G62 2.4 83.9 1.0 C8 B:G62 3.3 84.0 1.0 C5 B:G62 3.4 83.3 1.0 OP2 B:C39 3.6 80.9 1.0 O6 B:G62 3.6 83.1 1.0 C6 B:G62 3.9 82.9 1.0 N9 B:G62 4.5 83.7 1.0 C4 B:G62 4.5 83.2 1.0 OP2 B:G62 4.6 91.4 1.0 P B:C39 4.6 81.2 1.0 OP2 B:U61 4.8 0.9 1.0 O5' B:C39 4.9 80.6 1.0 C5 B:U61 5.0 94.2 1.0

L.Huang, A.Serganov, D.J.Patel. Structural Insights Into Ligand Recognition By A Sensing Domain of the Cooperative Glycine Riboswitch. Mol.Cell V. 40 774 2010.
ISSN: ISSN 1097-2765
PubMed: 21145485
DOI: 10.1016/J.MOLCEL.2010.11.026